Design and Nested Hierarchies

even if there is no nested hierarchy in nature evolution will be just fine.

I hate to keep using quotes from Romanes essay, but it is a gold mine. Romanes takes the same approach that I have seen @swamidass and others push forward, that science is a limited explanation that applies to immediate causes.

There is an interesting bit of psychology that is woven into these discussions. At times, people put forward this false dichotomy of Nature or God. I have seen both theists AND atheists use this argument, so I won’t be throwing rocks from our glass grange hall. This is why PS (and BioLogos for that matter) are so refreshing because it is a place where both theists and atheists can agree about the limits of science and evidence, and find some common ground.

Does evolution disprove intelligent design in a philosophical or epistemological sense? No. Science can’t make any ontological claims, although some may extrapolate from science to reach those conclusions. However, if intelligent design is true then it was done through natural processes just like the rest of nature. Far be it for an atheist to judge another’s theology, but a deity who is sovereign over all of nature seems more divine and dignified than a deity who has to constantly tweak the creation to get the results he wants.

I don’t share that belief but really do respect it.


I agree 1000%. You probably can understand why I have often wondered why some of my Young Earth Creationist friends have such a small view of God and his sovereignty.

That is my view. And before some of my Christian brethren might possibly accuse me of rejecting miracles and supernatural intention entirely, that assumption is both untrue and a non sequitur. (Also, I always wince a bit when someone misunderstands deism and applies that label to my view. However, I will admit that the deism label is often abused in that way.)


Amen. Not only is ID not science, it is horrible theology.

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I’ve always been very disappointed that Biola University has so heavily promoted ID theology. I fear it will continue to damage their reputation. Talbot Seminary has been an excellent school.

My position regarding the rarity of functional islands for complex solutions in the sequence space is advocated, among many others, by people like @guppio, Meyer, Axe and Gelernter. Would you say that these scholars are irrational?
Regarding this topic, @gpuccio has written a very interesting piece (see below). You may disagree with him, but if you read his piece carefully and without prejudice, you will have no choice but to acknowledge the rationality of his arguments. At the same time, I understand your anxiety, for the stakes are immense. Indeed, if functional islands for complex functions are rare, ID wins and blind, unguided evolution is dead.

They are wrong, at a minimum. I don’t think @gpuccio has the knowledge do know that he is wrong, but I have to wonder about those with actual scientific training. Surely they know that sequence conservation can’t be used to determine the total sequence space for a given function, or the total function space that is available at any point in a fitness landscape. What I see is one long continuous Sharpshooter fallacy.

As I stated elsewhere, if they had a real method for measuring functional information then they would be able to do so for a random sequence. They can’t do that.

Then please tell us how you can rationally measure the total number of sequences that will produce a specific function by looking at how many residues can be sequentially changed in a single protein.


Yes, I would.

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I’am sorry to tell you this, but it is clearly irrational to hold that these scholars are irrational.

I’ve read it before. It’s flatly wrong of course. There are no targets in evolution.

You may disagree with him, but if you read his piece carefully and without prejudice, you will have no choice but to acknowledge the rationality of his arguments.

I have read it carefully and without prejudice, and his argument flat out fails. It’s so simple to see why. The things that evolve, evolve due to a combination of chance (historical contingency in the types of mutations that happens to occur), and selection. Selection isn’t towards any particular thing(hence not towards any targets), it’s just towards fitness. What happens to have a positive effect on fitness isn’t known beforehand by any organism, or by the process of mutation.

There was never a search for some particular gene, or sequence, or mutation(so no targets). Mutations occurred, and they had the phenotypic effects that they did which in turn affected their propensity to stick around and rise in frequency in coming generations. Some particular sequence (whether that is a protein coding gene or not) is in this way a historically contingent outcome, not a target. Down the line, any particular long such series of accumulating mutations will look like something that was unlikely to have happened. But that doesn’t make it a target.

In fact, you yourself agrees that looking at historically contingent outcomes of accumulating mutations as extremely unlikely targets commits the Texas sharpshooter fallacy. Let me remind you:

As was exactly my point.

So here you are, looking at some particular protein, or another genetic sequence, you calculate it would be unlikely for some accumulating series of mutations to result in that sequence(thus treating it as a target), and then you declare it couldn’t have happened. But as you correctly saw back then, that argument commits the Texas sharpshooter fallacy.


Your position should be based on evidence. How many of the >5000 papers on catalytic antibodies have you read?

I wouldn’t call any of them “scholars” in this field.

Are you saying that I am irrational? I have more experience studying the effects of sequence changes on protein function than all of them combined.

Science is about evidence, not arguments that avoid most of the evidence.

Your true colors are showing. I want to know the truth. You want to WIN. Which of us is more likely to be irrational?


First question: have you read it?

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You haven’t detected any design, and what’s the problem with discovering God through the amazing things we discover through the scientific method?

No design has been detected and there’s not even any evidence, much less hard evidence, that DNA was designed.

How can anything “show strong design detection”? Isn’t detection the action you’re claiming to be actively doing? Or are you just using the term incoherently to rationalize your inaction in a Freudian slip?

Indeed, but neither you nor anyone else in the ID movement is doing anything remotely related to seeking. You’re just claiming to have already found everything while sitting in your easy chair and arguing on the internet or reading books by people who have never done actual science or who have quit doing active science.

We, the people whom you claim understand biology less than you do, are the seekers.


Are you kidding ?
Of course I have read it, several time!
Second question : and you, have you read it? I doubt it, for any unbiased person, even if he may disagree with @gpuccio’s arguments, cannot deny that he is a rational person that uses rational arguments.
To take just one example, he demonstrated wonderfully that people who charge him of committing the sharpshooter fallacy are dead wrong.

That would be a No True Scotsman argument because you are judging a person’s rationality by whether they agree with @gpuccio.


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See the first part of @gpuccio’s piece.

I am not judging a person’s rationality by whether they agree with @gpuccio, but rather by whether they recognize that he is using rational arguments. Do you see the difference?

His analogy with the green vs brown bricks in the wall is apposite. He’s saying there are no shots in the brown bricks, but that’s exactly what there are. Countless of them. Most non-coding DNA is essentially the brown bricks, and most mutations (which could be called the “shots”) end up in brown bricks. But Gpuccio is drawing circles around protein-coding genes(or other functional sequences), aka the shots in the green bricks.

But in his analogy there have been no shots at the brown bricks. He says all the shots are in the green bricks, basically ignoring or forgetting all the shots in the brown bricks. That’s just flat out incorrect.

So he’s committing the Texas sharpshooter fallacy.

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@gpuccio doesn’t address the argument we are making. By focusing on just one protein and its descendants you are missing all of the other possible starting targets for that function. Even more, at any one point there are many different functions that could increase fitness, not just the one that was found.


You are assuming that his arguments are rational, and then dismissing people who disagree with you.